COVID-19 Research
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COVID-19 Research Solutions

COVID-19 Research Solutions

Prosigna Score / ROR Score:

The ROR Score has been validated to predict the risk of recurrence of disease in ER+ breast cancer after surgery and treatment with 5 years of endocrine therapy. The ROR score depends upon the biology of the intrinsic subtypes, the proliferation score of the tumor, and the tumor size as shown in the equation below:

ROR = aRLumA + bRLumB + cRHer2 + dRBasal + eP + fT

Each of the R variables in the equation above indicate the Pearson correlation coefficient of the PAM50 expression profile for the tumor compared to each of the prototypical centroids for the intrinsic subtypes shown in the heatmap below. P is the proliferation score, which is the average gene expression profile of genes associated with cell-cycle progression and T is the tumor stage.

Figure: Heatmap of PAM50 genes by subtype. Red is higher expression and green is lower expression

COVID-19 Research Solutions
  • In several recently published studies, nCounter® gene expression assays such as the immunology panel and inflammation panel were used to describe the dynamic and varied host response that shapes the progression of COVID-19. Building on this success,

  • NanoString developed the 785-plex Human and mouse host response panel as well as a Coronavirus Panel Plus spike-in, enabling measurement of the SARS-CoV-2 virus, additional human coronaviruses, and the human ACE2 receptor RNA in addition to the measurement of host immune response genes.  The Coronavirus Panel Plus can be spiked-in to any gene expression panel, expanding the range of biology that can be studied with COVID-19 samples.

  • The GeoMxDigital Spatial Profiler (DSP) enables simultaneous high-plex spatial analysis of pathogens and the host response with FFPE and fresh frozen tissue.

  • The GeoMxCOVID-19 Immune Response Atlas facilitates spatial studies of the SARS-CoV-2 virus and the host response with over 1,800 RNA targets.

  • The COVID-19 GeoMx-formatted Antibody, developed in partnership with Abcam, is a five-antibody custom protein panel that can be run alongside GeoMxprotein assays. These assays include SARS-CoV-2 viral markers and the ACE2 receptor, among other receptors, proteases, cell markers, and viral response markers, and are available through the GeoMx Technology Access Program.

nCounter Host Response Panel

The 785-plex nCounter Host Response Panel contains probes for human or mouse genes involved in the host response to pathogens.  Best suited for use with blood samples, the Host Response Panel covers the five stages of infection: incubation, prodromal period, peak illness, decline, and convalescence, with probes for genes involved in the innate and adaptive immune response, interferon signaling, host susceptibility, and homeostasis.  The panel includes NanoString’s unique immune cell typing signatures for quantifying the relative abundance of 14 different immune cell types, and data from the panel can be easily analyzed in minutes with the nSolver Data Analysis Software or the cloud-based ROSALIND™ by OnRamp BioThe panel is ideally suited for use to study SARS-CoV-2 but can be easily used to study other types of pathogens.

nCounter Host Response Panel

GeoMx DSP COVID-19 Protein and RNA Analysis

  • Rapidly perform high-plex spatial analyses of the host response in FFPE or fresh frozen tissue using the  GeoMx Digital Spatial Profiler (DSP). NanoString’s GeoMx DSP platform enables high-plex protein and RNA experiments in key areas of biology such as molecular response, cellular (immune) response, tissue damage, and drivers of individual susceptibility to severe forms of disease.

  • The GeoMx COVID-19 Immune Response Atlas, a ~1,850-plex RNA assay, enables spatial studies of the SARS-CoV-2 virus and host response. RNA targets include COVID-19 receptors and proteases, pulmonary alveolar type I and II markers, lung biology markers, viral response markers, and SARS-CoV-2 probes. RNA targets are profiled simultaneously using the GeoMx DSP and an Illumina next-generation sequencer (NGS) for readout. Users can run ACD RNAscope™ probes alongside GeoMx RNA probes to identify regions of interest.

  • A five-antibody custom, ready-to-go protein panel, with receptor, protease, and viral markers is available through the GeoMx Technology Access Program or for order through Abcam. This  COVID-19 GeoMx-formatted Antibody  is run with the 20-plex GeoMx Immune Cell Profiling Core (plus controls) with readout on the nCounter Analysis System. Users can add up to six 10-plex modules including the Immune Activation Status, Immune Cell Typing, and/or Cell Death modules to more deeply profile proteins involved in T cell activation and cell death. NanoString scientists can recommend commercially-available markers for lung epithelium, nasal epithelium, immune response markers, and the viral spike protein.

The eight essential components of stem cell biology

Stemness
Pluripotency
Regulatory Signaling
Epigenetics
Mechano-Signaling
Metabolism
Differentiation Signaling
Lineage Specification

Stem Cell Renewal:

  • Stem Cell Prolifiration

  • Cell Cycle

  • Senescence/Quiescence

  • Autophagy

  • Apoptosis

  • Anti-Apoptosis

  • PSC Pluripotency Markers and Regulators

  • Naive State/Primed State

Regulatory Pathways:​

  • Wnt/B-catenin Pathway

  • Hedgehog Signaling

  • AP-1 Signaling

  • PI3K-AKTmTOR Pathway

  • MAPK Pathway

  • JAK/STAT Pathway

  • Notch Signaling

Epigenetic Mechanism:

  • DNA Methylation

  • Histone Acetylation & Methylation

Mechano-Signaling:

  • Rho/ROCK Signaling

  • integrin/Cadherin Signaling

  • Hippo Pathway

Metabolism:

  • Oxidative Stress Response

  • Hypoxia Response

  • Amino Acid Metabolism

  • Fatty Acid Metabolism

  • Glutamine Metabolism

  • Glucose Metabolism

Differentiation Signaling and Pathways:

  • TGFB Signaling

  • Cytoskeletal Reorganization

  • MET/EMT Signaling

  • HOX Gene Activation

Differentiation Lineage:

  • Endodermal /Ectodermal /Mesodermal Lineage Markers

  • Key Somatic Cell Types

Custom & Clinical Products

Assay Type
Product
Maximum Targets
Daily Sample Throughput
Analytes Offered
Common Applications

Custom codeSets

Elements TagSets

PlexSet Reagents

Self-assembled, interchangeable probes, optimized for smaller validation projects with maximum flexibility

Self-assembled, interchangeable probes for high-throughput, sample multiplexing projects

User-designed, turn-key solution that comes ready-to-use

216

96

800

24-96

24-96

192-1152

mRNA, CNV, Fusions

mRNA, Fusions

mRNA, miRNA, CNV, Fusions

Cell line drug screen, biomarker development, infectious disease

Gene Signature Development

Model Organism, Microbes, Agriculture

SKU
Description
Pack Size

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